Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,153,482 T→C 10.8% K254K (AAA→AAG)  treR_3 ← HTH‑type transcriptional regulator TreR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,153,4820TC10.8% 92.3 / 3.5 37K254K (AAA→AAG) treR_3HTH‑type transcriptional regulator TreR
Reads supporting (aligned to +/- strand):  ref base T (20/13);  new base C (2/2);  total (22/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.23e-01

AGCATCTGTTGTATCTCTTCCATCGCGCATTGGCCAGCTTCAAAATAATTATAATGAATTGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCATCTACTTGCTCCACATTTTCCAAAACATTTGCAACATCTTTTTGTGCTTCCACATAAGTAAAATTTGTTTCATGTATATT  >  USA300TCH1516_ALE/2153342‑2153622
                                                                                                                                            |                                                                                                                                            
aGCATCTGTTGTATCTCTTCCATCGCGCATTGGCCAGCTTCAAAATAATTATAATGAATTGTTTTTATCGATGGAGAAAATAATAGTGTCATAAGGTCACCACCAAAACCTTATATTTGATGTGGTTTCATAACATCtttt                                                                                                                                              <  2:129371/141‑1 (MQ=255)
 gCATCTGTTGTATCTCTTCCATCGCGCATTGGCCAGCTTCAAAATAATTATAATGAATTGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGTGTTCATAACATCttttt                                                                                                                                             >  2:323687/1‑141 (MQ=255)
    tCTGTTGTATCTCTTCCATCGCGCATTGGCCAGCTTCAAAATAATTATAATGAATTGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTCTTAt                                                                                                                                          >  2:130402/1‑141 (MQ=255)
    tCTGTTGTATCTCTTCCATCGCGCATTGGCCAGCTTCAAAATAATTATAATGAATTGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTCTTAt                                                                                                                                          >  1:328089/1‑141 (MQ=255)
         tgtATCTCTTCCATCGCGCATTGGCCAGCTTCAAAATAATTATAATGAATTGTTTTTAGCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGaa                                                                                                                                     >  1:218859/1‑141 (MQ=255)
           tATCTCTTCCATCGTGCATTGGCCAACTTCAAAATAATTATAATGAACTGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGaata                                                                                                                                   <  1:214794/141‑1 (MQ=255)
             tctcTTCCATCGAACATTGGCCAGCTTCAAAATAATTATAATGAATTGTTTTTATCGATGAAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGaataat                                                                                                                                 >  2:271011/1‑141 (MQ=255)
                 ttCCATCGCGCATTGGCCAGCTTCCAAATAATTATAATGAATTGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGAATAATAttt                                                                                                                             <  2:224097/141‑1 (MQ=255)
                 ttCCATCGCGCATTGGCCAGCTTCAAAATAATTATAATGAATTGTTTTTATCGATGGAGCCACTAATTGTGTCATTGGGTCACCACCAAAACCATATACTTGATGTGGTTTCATAACATCTTTTTTATCAGCATACTAttt                                                                                                                             >  1:62323/1‑141 (MQ=255)
                 ttCCATCGCGCATTGGCCAGCTTCAAAATAATTATAATGAATTGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCCAAACCACAGAATTGATGTGGTTTCATAACATCTTTTTTATCAGAATAATAttt                                                                                                                             >  1:81097/1‑141 (MQ=255)
                 ttCCATCGCGCATTGGCCAGCTTCAAAATAATTATAATGAATTGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAAAATCTTTTTTATCAGACTAGTtttt                                                                                                                             >  1:62376/1‑141 (MQ=255)
                     aTCGCGCATTGGCCAGCTTCAAAATAATTATAATGAATTGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCACAACCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGAATAATATTTATAg                                                                                                                         >  1:350662/1‑141 (MQ=255)
                      tCGCGCATTGGCCAGCTTCAAAATAATTATAATGAATTGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGTATAATATTTATAgg                                                                                                                        <  1:191524/141‑1 (MQ=255)
                          gcATTGGCCAGCTTCAAAATAATTATAATGAATTGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGAATAATATTTATAGGCAGc                                                                                                                    >  1:294021/1‑141 (MQ=255)
                                      ttCAAAATAATTATAATGAATTGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTAATGTGGTTTCATAACATCTTTTTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGt                                                                                                        <  1:67650/141‑1 (MQ=255)
                                       tCAAAATAATTATAATGAATTGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGAATAATATTTATAGTCAGCTAATGCAATCGtt                                                                                                       >  2:77789/1‑140 (MQ=255)
                                       tCAAAATAATTATAATGAATTGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGTa                                                                                                       >  2:226300/1‑141 (MQ=255)
                                               atTATAATGAATTGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGAATAATATTAATAGGCAGCTAATTCAATCGTATCATTTGc                                                                                               >  2:37445/1‑141 (MQ=255)
                                                ttATAATGAATTGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATGACATCTTTTTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCt                                                                                              >  2:99688/1‑141 (MQ=255)
                                                           tGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACAACCAAAACCAAATATTTGATGTGGTTTCATAACATCTTTTTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGc                                                                                   >  1:301302/1‑141 (MQ=255)
                                                              ttttATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCATc                                                                                >  1:172705/1‑141 (MQ=255)
                                                              ttttATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCATc                                                                                <  1:299391/141‑1 (MQ=255)
                                                               tttATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTCTTATCAGAATAATATTTATAGGCAGCTAATGCAATCTCATCACTTCCCCCAACAACCGCATCt                                                                               <  2:328089/141‑1 (MQ=255)
                                                               tttATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTCTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCATCt                                                                               <  1:130402/141‑1 (MQ=255)
                                                                                  aTTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCATCTACTTGCTCCACATTTTCCa                                                            >  1:150583/1‑141 (MQ=255)
                                                                                  aTTGTGTCATAGGGTCACCACCAAAACCATATATTTGATGTGGCTTCAAAACATCTTTTTTATCAGAATAATATTTATAGGCAGCTGATGCAATCGTATCGGTTGCTCCAACAACCGCATCCACTTGCTCCACATCTTCCa                                                            >  2:288214/1‑141 (MQ=255)
                                                                                       gtCATTGGGTCACCACCAAAAACATATATTTGATGTGGTATAATAAAAAATTTTTTATCAGAATAATATTTATTGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCATCTACTTGCTCCACATCTTCCAAAAcc                                                       >  2:318275/1‑140 (MQ=255)
                                                                                             gggTCCCCACCAAAACCATATATTTGATTTGGTTTCATCACATCTTTTTCATCAGACAAATATTTATAGGCAGCTAACGCAATCGTAACAGTTGCTCCCACAACACCATCTACTTGCTCCACATTTTCCCAAACATTTGCa                                                 <  2:62376/141‑1 (MQ=255)
                                                                                             gggTCACCACCAAAATCATAGTCTTGATGTGGTTGCATCACATCTTTTTTATCAGAGTGATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCCACAGCCGCATCTACTTGCTCCACATTTTCCAAAACATTTGCa                                                 <  2:62323/141‑1 (MQ=255)
                                                                                             gggTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCATCTACTTGCTCCACATTTTCCAAAACATTTGCa                                                 <  2:81097/141‑1 (MQ=255)
                                                                                                    caccaAAACCAAATATTAGATGTGGTTTCATAACATCTTTTTTAACAGAACAATATTTATAGGCAGCTAATGCAACCGTATCAGTTGCTCCAACAACCGCATCTACTTGCTCCACATTTCCCAACACATTTGCAACATCtt                                          <  2:335146/141‑1 (MQ=255)
                                                                                                     cccaAAACCCTATATTTGATGTGGGTTCATAACATCTTTTTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCATCTACTTGCTCCACATTTTCCAAAACATTTGCAACATCttt                                         <  1:295682/140‑1 (MQ=255)
                                                                                                        aaatCCATATATTTGAGGTCGTTTCATAACATCTTTTTTATCAGAATAATATTCATAGGCAGCTAACGCAATCGTATCAGTCGCTCCAACAACCGCATCTACTTGCTCCACATTTTCCAAAACATTTGCAACATCTTTTtg                                      <  2:68417/141‑1 (MQ=255)
                                                                                                        aaaaCCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCATCTACTTGCTCCACATTTTCCAAAACATTTGCAACATCTTTTtg                                      <  2:172705/141‑1 (MQ=255)
                                                                                                           aCCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCATCTACTTCCTCCTCATTTTCGCAAACATTTGCAACAACCTTTTGTGc                                   >  2:187022/1‑141 (MQ=255)
                                                                                                             cATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCACCTACTTGCTCCACATTTTCCAACACATTGGCAACATCTTTTTGTGCtt                                 >  1:102448/1‑141 (MQ=255)
                                                                                                                       aTGTGGTTTCATAACATCTTTTTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCATCTACTTGCTCCACATTTTCCAAAACATTTGCAACATCTTTTTGTGCTTCCACATAAGt                       >  1:44930/1‑141 (MQ=255)
                                                                                                                         gtgGTTTCATAACATCTTTTTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCATCTACTTGCTCCACATTTTCCAAAACATTTGCAACATCTTTTTGTGCTTCCACATAAGTaa                     <  1:271638/141‑1 (MQ=255)
                                                                                                                          tgGTTTCATAACATCTTTTTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCATCTACTTGCTCCACATTTTCCAAAACATTTGCAACATCTTTTTGTGCTTCCACATAAGTaaa                    >  1:320982/1‑141 (MQ=255)
                                                                                                                                           ttttATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCATCTACTTGCTCCACATTTTCCAAAACATTTGCAACATCTTTTTGTGCTTCCACATAAGTAAAATTTGTTTCATGTatat   >  2:184163/1‑141 (MQ=255)
                                                                                                                                           ttttATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCATCTACTTGCTCCACATTTTCCAAAACATTTGCAACATCTTTTTGTGCTTCCACATAAGTAAAATTTGTTTCATGTatat   >  2:100254/1‑141 (MQ=255)
                                                                                                                                            tttATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCATCTACTTGCTCCACATTTTCCAAAACATTTGCAACATCTTTTTGTGCTTCCACATAAGTAAAATTTGTTTCATGTATAtt  >  2:323930/1‑141 (MQ=255)
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AGCATCTGTTGTATCTCTTCCATCGCGCATTGGCCAGCTTCAAAATAATTATAATGAATTGTTTTTATCGATGGAGACACTAATTGTGTCATTGGGTCACCACCAAAACCATATATTTGATGTGGTTTCATAACATCTTTTTTATCAGAATAATATTTATAGGCAGCTAATGCAATCGTATCAGTTGCTCCAACAACCGCATCTACTTGCTCCACATTTTCCAAAACATTTGCAACATCTTTTTGTGCTTCCACATAAGTAAAATTTGTTTCATGTATATT  >  USA300TCH1516_ALE/2153342‑2153622

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑